Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
14,867
datasets available to search
ShareScore release 0.9.0
Dataset results
14,867 results for “Determinants”
Testing the Fidelity of Paleopole Determinations from Multidirectionally Magnetized Lunar Crustal Anomaly Source Bodies
<p>Code and data for "Testing the Fidelity of Paleopole Determinations from Multidirectionally Magnetized Lunar Crustal Anomaly Source Bodies ". See readme.txt</p>
Structural equation modeling reveals determinants of fitness in a cooperatively breeding bird
<p>Even in well-studied organisms, it is often challenging to uncover the social and environmental determinants of fitness. Typically, fitness is determined by a variety of factors that act in concert, thus forming complex networks of causal relationships. Moreover, even strong correlations between social and environmental conditions and fitness components may not be indicative of direct causal links, as the measured variables may be driven by unmeasured (or unmeasurable) causal factors. Standard statistical approaches, like multiple regression analyses, are not suited for disentangling such complex causal relationships. Here, we apply structural equation modeling (SEM), a technique that is specifically designed to reveal causal relationships between variables, and which also allows to include hypothetical causal factors. Therefore, SEM seems ideally suited for comparing alternative hypotheses on how fitness differences arise from differences in social and environmental factors. We apply SEM to a rich data set collected in a long-term study on the Seychelles warbler (Acrocephalus seychellensis), a bird species with facultatively cooperative breeding and a high rate of extra-group paternity. Our analysis reveals that the presence of helpers has a positive effect on the reproductive output of both female and male breeders. In contrast, per capita food availability does not affect reproductive output. Our analysis does not confirm earlier suggestions on other species that the presence of helpers has a negative effect on the reproductive output of male breeders. As such, both female and male breeders should tolerate helpers in their territories, irrespective of food availability.</p>
Data and Scripts for Schweiger et al. (2021) "Chemical properties of key metabolites determine the global distribution of lichens"
<p>Data and Scripts for Schweiger et al. (2021) "Chemical properties of key metabolites determine the global distribution of lichens".</p> <p>A detailed description of the individual files is provided in the "Schweiger-et-al-DataPublication-Index-Submissionfiles.txt" file.</p> <p>Summary of the study:</p> <p>In lichen symbioses, fungal secondary metabolites provide UV protection on which certain lichen algae such as trebouxioid green algae sensitively depend. These metabolites differ in their UV absorbance capability and solvability, and thus vary in their propensity of being leached from the lichen body by high precipitation and temperatures, with still unknown implications for the global distribution of lichens. In this global study, we show that the occurrence and chemical properties of fungal-derived metabolites are of eco-evolutionary significance for the global, latitudinal distribution of lichenized Trebouxiophyceae. This might represent an indirect environmental adaptation in which the mycobiont invests to protect the trebouxioid photobiont from harsh environmental conditions and, by doing this, secures its efficient source of photosynthetic carbon.</p>
Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network
<p>In this repository we provide raw and processed datasets for the article: “Genome-wide gene expression noise in <em>Escherichia coli </em>is condition-dependent and determined by propagation of noise through the regulatory network<strong>” </strong>by Arantxa Urchueguía, Luca Galbusera, Dany Chauvin, Gwendoline Bellement, Thomas Julou and Erik van Nimwegen.</p> <p>A preprint is available under the following DOI: <a href="https://doi.org/10.1101/795369">https://doi.org/10.1101/795369</a>. </p> <p>The repository consists of the following datasets: </p> <p><strong>1. preprocessed_datasets.zip(~22GB)</strong></p> <ul> <li>This dataset contains raw data from the flow cytometry experiments (FACS Canto II, BD Bioscience) in all measured conditions in RData format. Raw fcs files were processed with the tools described in the publication ''Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria" published here: <a href="https://doi.org/10.1371/journal.pone.0240233">https://doi.org/10.1371/journal.pone.0240233</a>. The tools themselves are available here: <a href="https://github.com/vanNimwegenLab/E-Flow">https://github.com/vanNimwegenLab/E-Flow</a>. Included in the files are the outputs of these processing tools together with all raw values that came directly from the flow cytometer. The file <em>directory_structure_in_preprocessed </em>contains information about how the files are organized.</li> </ul> <p><strong>2. info_files: </strong>This is a set of csv files containing detailed information about the experiments done to acquire the preprocessed_datasets as well as annotation files that we used to retrieve promoter information. </p> <p><strong>3. processed_datasets:</strong> These files correspond to the processed datasets from the raw Rdata files under 1 above. The processed data provide mean and variance estimates in fluorescence of E.coli promoters across the different growth conditions. Note that we discarded flow cytometry measurements from promoter/growth-condition combinations that contained abnormal fluorescence distributions (due to contamination) as well as measurements from reporters with annotation mismatches. The folder contains the following clean dataset files that were used in the paper:</p> <ul> <li><strong>FULL_dataset_mean_var_wreplicates:</strong> In this dataset we include the processed means and variances (in both logarithmic and linear scale) of all promoters in each condition. Included as well are replicate measurements for some conditions.. We also include the name and Blattner number of the gene immediately downstream of each promoter, the DNA sequence of each promoter, and regulatory information (number of unique inputs for transcription factors sites and their names) which we obtained from RegulonDB v 10.5 (<a href="https://doi.org/10.1093/nar/gky1077">https://doi.org/10.1093/nar/gky1077</a>). </li> <li><strong>dataset_with_noise_estimates: </strong>In this dataset we provide noise estimates for all promoters expressed above an expression threshold (mean GFP fluorescence at least as large as autofluorescence). Note that the noise estimate correspond to the difference between the promoter’s variance in log-expression and the minimal variance as a function of its mean expression (i.e. the so called noise floor was subtracted). Apart from the mean, variance, noise and promoter features (sequence, name of gene downstream, number of unique regulatory inputs and name of the TFs binding), we also include the parameters used for fitting the minimal noise, i.e. noise floor, in each of the conditions. </li> <li><strong>time_course_data_SI</strong>: This dataset contains mean and variance measurements of one of the plates of the library measured at different time points during growth in Minimal media 0.4M NaCl: 0h (just after dilution), 1h, 2h, 3h, 5h, 6.5h, 8.5h, 10h and 11h. </li> <li><strong>growth_curves_SI</strong>: Growth data (OD<sub>600</sub> as a function of time) for a subset of the promoters from the library across different growth conditions.</li> <li><strong>singlecell_areas_SI: </strong>Single-cell areas estimated using agar patches of cells growing in each condition. Each row of the table contains data for a single-cell. </li> <li><strong>synthetic_promoters_dataset: </strong>This dataset contains mean, variance and noise measurements of a set of constitutive promoters from <a href="https://doi.org/10.7554/eLife.05856.001">https://doi.org/10.7554/eLife.05856.001</a> across different conditions.</li> <li><strong>MARA_results:</strong> All transcription factor activities results explaining measured noise levels in each condition. This data has been obtained after performing Motif Activity Response Analysis on the noise levels of all measured promoters in each condition.</li> </ul>
Fig. 2 in Age Determination And Some Growth Parameters Of A Rana Ridibunda Population In Turkey
Fig. 2. Cross-section taken at the middle of the diaphysis of Rana ridibunda, a male, 58 mm SVL, 4 RL (scale: 108 µm)
Accurate Vertical Ionization Energy and Work Function Determinations of Liquid Water and Aqueous Solutions
<p>Dataset underlying report about a protocol to determine absolute binding energies from photoionization of liquid microjet samples, published as <a href="https://doi.org/10.1039/D1SC01908B">Accurate vertical ionization energy and work function determinations of liquid water and aqueous solutions</a>.</p>
Determinant Factors in Systematic Review of Biomedical Engineering Topics
<p>Students and researchers around the world are increasingly turning to literature reviews. Review articles give you a broad picture of the field and help synthesize published research that is expanding at a rapid pace.</p> <p>Professionally crafted literature reviews, whether written by a student in class or by an experienced researcher for publication, should aim to add to the literature rather than detract from it. This is not an easy feat, but it is a necessary one.<br> Systematic reviews aim to identify, evaluate, and summarize the findings of all relevant individual studies on a related topic; which makes the available evidence more accessible to decision makers.</p> <p>Research Question<br> • Provide enough detail so that the audience can easily understand your purpose without the need for additional explanation.</p> <p>• It is not answered with a simple “yes” or “no”, but requires synthesis and analysis of ideas and sources before writing a response.</p> <p>Search strategy<br> • Organized structure of key terms used to search databases.</p> <p>• Combine key concepts to get accurate results.</p> <p>Inclusion and exclusion criteria<br> They are determined after the research question is established, usually before the search is performed, however, scoping searches may be necessary to determine the appropriate criteria</p> <p>Synthesis<br> • A review matrix and summary tables are convenient ways to quickly summarize and reorganize qualitative information and observations to achieve a preliminary outline.</p> <p>Systematic reviews serve several critical functions</p> <p>Provide synthesis of the state of knowledge in a field, from which future research priorities can be identified;</p> <p>Addressing questions that could not otherwise be answered by individual studies;</p> <p>Identify problems in primary research that should be rectified in future studies;Generate or evaluate theories about how or why phenomena occur.</p>
Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions
<p>Polysaccharide utilization loci (PULs) in the human gut microbiome have critical roles in shaping human health and ecological dynamics. We develop a CRISPR-FnCpf1-RecT genome-editing tool to study 23 PULs in the highly abundant species <em>B. uniformis</em> (BU). We identify the glycan-degrading functions of multiple PULs and elucidate transcriptional coordination between PULs that enables the population to adapt to the loss of PULs. Exploiting a pooled BU mutant barcoding strategy, we demonstrate that the <em>in vitro</em> fitness and the colonization ability of BU in the murine gut is enhanced by deletion of specific PULs and modulated by glycan availability. We show that BU PULs can mediate complex glycan-dependent interactions with butyrate producers that depend on the mechanism of degradation and the butyrate producer glycan utilizing ability. In sum, PULs are major determinants of community dynamics and butyrate production and can provide a selective advantage or disadvantage depending on the nutritional landscape. </p>
Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe
<p>Context. Plant populations in agricultural landscapes are mostly fragmented and their functional connectivity often depends on seed and pollen dispersal by animals. However, little is known about how the interactions of seed and pollen dispersers with the agricultural matrix translate into gene flow among plant populations.</p> <p>Objectives. We aimed to identify effects of the landscape structure on the genetic diversity within, and the genetic differentiation among, spatially isolated populations of three temperate forest herbs. We asked, whether different arable crops have different effects, and whether the orientation of linear landscape elements relative to the gene dispersal direction matters.</p> <p>Methods. We analysed the species' population genetic structures in seven agricultural landscapes across temperate Europe using microsatellite markers. These were modelled as a function of landscape composition and configuration, which we quantified in buffer zones around, and in rectangular landscape strips between, plant populations.</p> <p>Results. Landscape effects were diverse and often contrasting between species, reflecting their association with different pollen- or seed dispersal vectors. Differentiating crop types rather than lumping them together yielded higher proportions of explained variation. Some linear landscape elements had both a channelling and hampering effect on gene flow, depending on their orientation.</p> <p>Conclusions. Landscape structure is a more important determinant of the species' population genetic structure than habitat loss and fragmentation <i>per se</i>. Landscape planning with the aim to enhance the functional connectivity among spatially isolated plant populations should consider that even species of the same ecological guild might show distinct responses to the landscape structure.</p>
Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities: discovery cohort meta data and parsed TCR repertoire data
<p>Meta data corresponding the the discovery cohort for the paper, "Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities" by Magdalena L Russell, Aisha Souquette, David M Levine, Stefan A Schattgen, E Kaitlynn Allen, Guillermina Kuan, Noah Simon, Angel Balmaseda, Aubree Gordon, Paul G Thomas, Frederick A Matsen IV, and Philip Bradley. These meta data include: </p> <p>(1) a file mapping the SNP data subject IDs to the TCR repertoire data subject IDs (gwas_id_mapping.tsv)<br> (2) a file including the PCAir PCs, self-reported ancestry, and genomic ancestry for each subject (all_pc_air.txt)<br> (3) a file including the PCAir variance explained by each PC (all_pc_air_variance.txt)<br> (3) a file including the SNP ID, chromosome, hg19 position, allele, rsid, and quality control metrics for each SNP in the SNP array (emerson_snp_rs_data.tsv)<br> (4) a file including IMGT genes and sequences used for parsing TCRB repertoire data (human_vj_allele_cdr3_nucseqs.tsv)<br> (5) a file including predicted TRBD2 allele genotypes for each subject (emerson_trbd2_alleles.tsv)<br> (6) Parsed TCRB repertoire data. These raw data were first published in Emerson et. al, <em>Nature Genetics </em>2017. (emerson_parsed_tcrb.tgz)</p> <p><strong>Corresponding discovery cohort raw TCR repertoire data is available here: </strong>https: //doi.org/10.21417/B7001Z (ImmuneACCESS database)<br> <strong>Corresponding discovery cohort SNP data is available here:</strong> https: //www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001918.v1.p1 (The database of Genotypes and Phenotypes, accession number: phs001918)<br> <br> <strong>Software tools designed to work with these data are available here:</strong> https://github.com/phbradley/tcr-gwas</p>
Determination of areas with release potential of snow avalanche in Sharr Mountains in the Republic of Kosovo
<p>Avalanches represent a very high risk in residential areas, road infrastructure, environment, and economy, and can have fatal consequences if the human factors do not take any action. Advances in geospatial technology and access to spatial data have enabled spatial analysis to assist in decision-making regarding spatial planning in avalanche-prone locations. Determining locations with snow avalanche discharge potential is a crucial step in the avalanche zoning process.</p> <p>This research deals with areas with snow avalanche potential disjunction, based mainly on topographic factors followed by meteorological ones. Topographic factors were mainly determined according to morphometric techniques, which are achieved through geographic information systems (GIS), as well as meteorological ones from statistical data and various processing of spatial and non-spatial data. Spatial analysis are also supported by geostatistical methods Fuzzy Logic and AHP, which in interaction with GIS have enabled the achievement of the purpose of this paper. The results from the spatial analysis have been verified based on comparison methods, such as the ROC method which was used during this final phase, in which the analysis has shown that the methods used in this research have given satisfactory results. As the main result, we obtained maps of areas with snow avalanche potential discharge in the study area relating to two geostatistical methods.</p>
Cation concentrations for LOD/LOQ determination
<p>Dataset to determine LOD/LOQ for cation concentrations measured with a Metrohm Compact IC.</p> <p>0.1 mg/L concentration of standard.</p> <p>MagIC-NET 3.3 Software was used for exporting the data to a .csv file.</p>
Tree size, microhabitat diversity and landscape structure determine the value of isolated trees for bats in farmland
<p>Isolated trees are increasingly recognised as playing a vital role in supporting biodiversity in agricultural landscapes, yet their occurrence has declined substantially in recent decades. Most bats in Europe are tree-dependent species that rely on woody elements in order to persist in farmlands. However, isolated trees are rarely considered in conservation programs and landscape planning. Further investigations are therefore urgently required to identify which trees – based on both their intrinsic characteristics and their location in the landscape – are particularly important for bats. We acoustically surveyed 57 isolated trees for bats to determine the relative and interactive effects of size, tree-related microhabitat (TreM) diversity and surrounding landscape context on bat activity. Tall trees with large diameter at breast height and crown area positively influenced the activity of <em>Pipistrellus pipistrellus</em> and small Myotis bats (<em>Myotis</em> spp.) while smaller and thinner trees favoured <em>M. myotis</em> activity. The diversity of TreMs that can be used as roosts had a positive effect on (i) <em>Barbastella barbastellus</em> activity only when trees were relatively close (10% within 100 radius scale). The potential benefits of isolated trees for bats result from ecological mechanisms operating at both tree and landscape scales, underlining the crucial need for implementing a multi-scale approach in conservation programs. Maintaining the largest and most TreM-diversified trees located in the most heterogeneous agricultural landscapes will provide the greatest benefits.</p>
The location and vegetation physiognomy of ecological infrastructures determine bat activity in Mediterranean floodplain landscapes
<p>Ecological infrastructures (EI), defined as natural or semi-natural structural elements, are important to support biodiversity and could play a crucial role in counteracting the well-known impacts of intensive agriculture. Yet, the importance of EI remains largely unexplored in Mediterranean agricultural landscapes and for species providing essential ecosystem services such as bats. Here, we evaluated the role of different EI types – in terms of location (riparian vs terrestrial) and vegetation physiognomy (woody vs non-woody) – in shaping bat guild activity in crop fields located in the floodplains of the Iberian Peninsula. We recorded 60,732 bat sequences in 96 crop fields and characterized 106 EI patches via an adaptation of the Biodiversity Potential Index (BPI). We found that the activity of mid-range echolocators (MRE) and long-range echolocators (LRE) was twofold higher when the nearest EI patch was riparian (i.e., contiguous to a watercourse) than when it was terrestrial. When assessing changes in bat activity in crop fields in relation to a gradient distance from EI types, our results revealed both distinct and similar effects of the location and vegetation physiognomy of the EI on bat guilds. For instance, while only the LRE guild positively responded to the proximity of woody EI, both MRE and LRE showed a marked increase of activity when increasing distances to non-woody EI, thus suggesting low bat activity levels near these features. Our habitat quality assessment also revealed that woody EI and riparian EI had higher biodiversity potential and related habitat quality, thus contributing to our understanding of bat responses to EI type in crop fields. As riparian areas are rarely targeted in biodiversity-friendly measures in farmland, we strongly recommend including riparian EI (especially the woody type) in conservation planning as they are crucial for both biodiversity conservation and ecosystem functioning.</p>
Standardization of Methodology of Light-to-Heat Conversion Efficiency Determination for Colloidal Nanoheaters
<p>Localized photothermal therapy (PTT) has been demonstrated to be a promising method of combating cancer, that additionally synergistically enhances other treatment modalities such as photodynamic therapy or chemotherapy. PTT exploits nanoparticles (called nanoheaters), that upon proper biofunctionalization may target cancerous tissues, and under light stimulation may convert the energy of photons to heat, leading to local overheating and treatment of cancerous cells. Despite extensive work, there is, however, no agreement on how to accurately and quantitatively compare light-to-heat conversion efficiency (ηQ) and rank the nanoheating performances of various groups of nanomaterials. This disagreement is highly problematic because the obtained ηQ values, measured with various methods, differ significantly for similar nanomaterials. In this work, we experimentally review existing optical setups, methods, and physical models used to evaluate ηQ. In order to draw a binding conclusion, we cross-check and critically evaluate the same Au@SiO2 sample in various experimental conditions. This critical study let us additionally compare and understand the influence of the other experimental factors, such as stirring, data recording and analysis, and assumptions on the effective mass of the system, in order to determine ηQ in a most straightforward and reproducible way. Our goal is therefore to contribute to the understanding, standardization, and reliable evaluation of ηQ measurements, aiming to accurately rank various nanoheater platforms.</p>
Data for the paper "Determining the value of preferred goods based on consumer demand in a home-cage based test for mice"
<p>All data related to the paper "Determining the value of preferred goods based on consumer demand in a home-cage based test for mice" will be made available to the scientific public here. The paper will be published soon in Behavioral Research Methods. </p>
Dataset of the determination of the topographic spatial resolution of a confocal point sensor with a type ASG material measure
<p>These original measurement data relate to the publication: J. Schaude, A. C. Gröschl, T. Hausotte: Effect of a Misidentified Centre of a Type ASG Material Measure on the Determined Topographic Spatial Resolution of an Optical Point Sensor, Metrology 2(1), p. 19-32, 2022, <a href="https://doi.org/10.3390/metrology2010002">https://doi.org/10.3390/metrology2010002</a>. Please refer to this open access publication for a detailed description of the measurement setup and procedure.</p> <p>All data are in ASCII-format. Each file contains four columns, where column one to three are the <em>x</em>, <em>y</em>, and <em>z</em>-coordinates of the positioning system and column four is the signal of the photodetector.</p> <p><strong>Content of the folders</strong></p> <p>10_Plane: Axial probings on 18 points just outside the grooves.</p> <p>20_Edges: Lateral probings from each point just outside the grooves in the direction of the roughly determined centre of the material measure.</p> <p>30_PlaneArea: Repeated axial probing on a plane area near the material measure.</p> <p>40_RadialMeasurement: Radial measurement of the material measure by lateral (radial) probings conducted on different heights (referring to the distance to the plane fitted to the measuring points of 10_Plane), and radii (referring to the centre of the circle fitted to the edges determined in 20_Edges). Each radial probing has its own data file, with the name of the data file being “radial_probing {radius in m} {height in m} {data and time of probing}.txt”.</p> <p>50_LineMeasurement: Lateral probings conducted on different heights (referring to the distance to the plane fitted to the measuring points of 10_Plane), different lateral offsets (referring to the centre of the circle fitted to the edges determined in 20_Edges) and on two angles (on the groove (0°) and the adjacent top level (10°)). Please refer to sec. 5.2 of the aforementioned publication for a detailed description. Each lateral probing has its own data file, with the name of the file being “lateral probing {angle in °} {offset in m} {height in m} {data and time of probing}.txt”.</p> <p><strong>Acknowledgement</strong></p> <p>This project 20IND07 TracOptic has received funding from the EMPIR programme co-financed by the Participating States and from the European Union’s Horizon 2020 research and innovation programme. Funder name: European Metrology Programme for Innovation and Research (EMPIR); Funder ID: 10.13039/10001413</p>
Datasets for "Comparison of multivariate ANOVA-based approaches for the determination of relevant variables in experimentally designed metabolomic studies"
<p><em><strong>Raw files of the LC-MS designed experiments.</strong></em></p> <p> </p> <p>* <strong>YEAST GROWTH DATASET</strong></p> <blockquote> <p><strong>A) Phospholipids extraction</strong></p> <p>- FosfoB1.raw</p> <p>- FosfoB3.raw</p> <p>- FosfoC2.raw</p> <p>- FosfoD1.raw</p> <p>- FosfoE1.raw</p> <p>- FosfoE2.raw</p> <p>- FosfoE3.raw</p> </blockquote> <p> </p> <blockquote> <p><strong>B) Sphingolipids extraction</strong></p> <p>- EsfingoB1.raw</p> <p>- EsfingoB2.raw</p> <p>- EsfingoC1.raw</p> <p>- EsfingoC2.raw</p> <p>- EsfingoC3.raw</p> <p>- EsfingoD1.raw</p> <p>- EsfingoD2.raw</p> <p>- EsfingoD3.raw</p> </blockquote> <p> </p> <p><strong>* ZEBRAFISH DATASET</strong></p> <blockquote> <p><strong>A) BPA study</strong></p> <p>Low BPA exposure</p> <p>- Low_BPA_A.d</p> <p>- Low_BPA_B.d</p> <p>- Low_BPA_C.d</p> <p>High_BPA_exposure</p> <p>- High_BPA_A.d</p> <p>- High_BPA_B.d</p> <p>- High_BPA_C.d</p> <p>Controls</p> <p>- Control_BPA_A.d</p> <p>-Control_BPA_B.d</p> <p>- Control_BPA_C.d</p> </blockquote> <p> </p> <blockquote> <p><strong>B) Estradiol study</strong></p> <p>Low E2 exposure</p> <p>- Low_E2_A.d</p> <p>- Low_E2_B.d</p> <p>- Low_E2_C.d</p> <p>High_E2_exposure</p> <p>- High_E2_A.d</p> <p>- High_E2_B.d</p> <p>- High_E2_C.d</p> <p>Controls</p> <p>- Control_E2_A.d</p> <p>-Control_E2_B.d</p> <p>- Control_E2_C.d</p> </blockquote> <p> </p> <p><strong>Funding:</strong> This research was funded by the Spanish Ministry of Science and Innovation (MCI, Grant CTQ2017-82598-P) and Severo Ochoa Project CEX2018-000794-S (funded by MCIN/AEI/ 10.13039/501100011033), and supported from the Catalan Agency for Management of University and Research Grants (AGAUR, Grant 2017SGR753). MPC was funded by a predoctoral FPU 16/02640 scholarship from the Spanish Ministry of Education and Vocational Training (MEFP). The 1290 LC system and 6545 XT QTOF instrumentation were provided to DS as gifts by Agilent Technologies through their Thought Leader program.</p>
Common Dynamic Determinants Govern Quorum Quenching Activity in N-terminal Serine Hydrolases
<ul> <li> <p>(File-01) Free enzymes molecular dynamics:</p> <ul> <li> <p>input parameters and topologies for aPGA, ecPGA and paPvdQ enzymes</p> </li> <li> <p>general input files for MD simulations in AMBER</p> </li> <li> <p>output restart files from minimization, equilibration and production runs</p> </li> <li> <p>output files from minimization, equilibration and production runs</p> </li> <li> <p>raw data for analysis and visualization:</p> <ol> <li> <p>protein backbone RMSD evolution</p> </li> <li> <p>binding cavity dynamics analysis</p> </li> <li> <p>principal component analysis of catalytic machinery (with states' representatives in PDF format)</p> </li> </ol> </li> </ul> </li> </ul> <p> </p> <ul> <li> <p>(File-02) Ligand-enzyme complexes molecular dynamics:</p> <ul> <li> <p>input parameters and topologies for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules</p> </li> <li> <p>general input files for MD simulations in AMBER</p> </li> <li> <p>output restart files from minimization, equilibration and production runs</p> </li> <li> <p>output files from minimization, equilibration and production runs</p> </li> <li> <p>raw data for analysis and visualization:</p> <ol> <li> <p>protein backbone RMSD evolution</p> </li> <li> <p>near-attack-conformation (NAC) stabilization</p> </li> <li> <p>HSLs RMSD evolution</p> </li> <li> <p>MM/PBSA binding energy estimation</p> </li> <li> <p>HSLs heavy atoms RMSF</p> </li> </ol> </li> </ul> </li> </ul> <p> </p> <ul> <li> <p>(File-03) Michaelis complex ensemble generation molecular dynamics:</p> <ul> <li> <p>input parameters and topologies for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules</p> </li> <li> <p>general input files for MD simulations in AMBER</p> </li> <li> <p>output restart files from ensemble generation production runs</p> </li> <li> <p>output files from ensemble generation production runs</p> </li> </ul> </li> </ul> <p> </p> <ul> <li> <p>(Files-04-06) Ligand-enzyme QM/MM steered molecular dynamics:</p> <ul> <li> <p>input parameters for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules</p> </li> <li> <p>ensemble of input restart files generated in stage 3</p> </li> <li> <p>general input files for QM/MM steered MD simulations in AMBER</p> </li> <li> <p>output restart files from QM/MM MD equilibration simulations and QM/MM steered MD simulations</p> </li> <li> <p>output files and output work from QM/MM steered MD simulations</p> </li> </ul> </li> </ul> <p> </p> <ul> <li> <p>(File-07) Ligand-enzyme QM/MM steered molecular dynamics data for analysis and visualization:</p> <ul> <li> <p>reaction states ensembles (in PDB format) extracted from QM/MM steered MD simulations with crucial distances measured</p> </li> <li> <p>evolution of the reaction coordinate elements in the first and second step of acylation</p> </li> <li> <p>representative states of the reaction stages for visualization (in PDB format)</p> </li> <li> <p>different dynamics of the residues gating access to acyl-binding cavity at TS1</p> </li> <li> <p>different dynamics of the residues gating overall access to active site at TS2a</p> </li> <li> <p>different system-dependent bending of the HSLs at TS1 and TS2a</p> </li> </ul> </li> </ul> <p> </p>
Morphological adaptations linked to flight efficiency and aerial lifestyle determine natal dispersal distance in birds
<p>Natal dispersal—the movement from birthplace to breeding location—is often considered the most significant dispersal event in an animal's lifetime. Natal dispersal distances may be shaped by a variety of intrinsic and extrinsic factors, and remain poorly quantified in most groups, highlighting the need for indices that capture variation in dispersal among species.</p> <p>In birds, it is hypothesized that dispersal distance can be predicted by flight efficiency, which can be estimated using wing morphology. However, the use of morphological indices to predict dispersal remains contentious and the mechanistic links between flight efficiency and natal dispersal are unclear.</p> <p>Here, we use phylogenetic comparative models to test whether hand-wing index (HWI, a morphological proxy for wing aspect ratio) predicts natal dispersal distance across a global sample of 114 bird species. In addition, we assess whether HWI is correlated with flight usage in foraging and daily routines.</p> <p>We find that HWI is a strong predictor of both natal dispersal distance and a more aerial lifestyle.</p> <p>Our results support the use of HWI as a valid proxy for relative natal dispersal distance, and also suggest that evolutionary adaptation to aerial lifestyles is a major factor connecting flight efficiency with patterns of natal dispersal.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.